The purpose of this article is to explore issues bearing on the question of the ontological reality of a certain category of exceptional human experiences. After briefly discussing the problem of metaphysics in a science of spirituality, I examine the supernatural nature of the natural and explain why normal science is not prohibited from evaluating supernatural claims. I then discuss how personal experience as a type of knowledge serves a heuristic function in the testing of metaphysical hypotheses by pointing out directions in which explanatory scientific theories might be found. I propose the construct of multidimensional reality as a solution to the problem of religious pluralism and explain why a state-specific science approach is appropriate for the development of an empirically (experientially) controlled metaphysics that takes experience in various states of consciousness as its empirical starting point. I conclude by discussing the function of metaphysical hypotheses in science and psychology and why the scientific realism of naturalistic inquiry may be the best approach to a viable and authentic science of spirituality.